Merge 2 armatures and 2 meshes then parent the armature to the mesh, without losing their weight paints?
this is probably a naming issue : 


the armature will create vertex groups with the bones names 
when you join the meshes groups with the same name get merged
when you join armatures bones will get new names if other with the same name exist
so you end up with one armature controlling both meshes


to avoid this ensure that your armature bones have different names before parenting each mesh to the armature